For a group that emphasizes thinking for oneself, it sure seems that there are a lot of rules for when it is or is not appropriate to vote on something. How about letting people decide for themselves what to vote on?

Agreed. Hence the "interpret as you see fit".

The fact is, to the site, an upvote means "please move this up the page", and a downvote or flag means "please remove this". At a most basic primal 2-year-old communication level, up is "yes" and down is "no".

This duality I find annoying - I want to be able to upvote with reasoning, even if there are just two vote types "Yes/No" and "Up/Down". Then I can show agreement or show that someone added to the thread but didn't say something I agree with.

The source is open. Go build that. Users will either respond to it, or they won't.

If I build it will HN implement it? I rather suspect not.